Mangroves are a vital ecosystem for coastal biodiversity and climate regulation but face increasing pressure from agriculture and aquaculture expansion. These threats promote high levels of degradation from direct land use change and hidden impacts from aquaculture effluents rich in nitrogen, phosphorus, and organic compounds. We developed a soil health index to detect different stages of mangrove ecosystem degradation by incorporating the concept of soil multifunctionality within a site-specific environmental context. We applied this index to four mangrove areas in the Amazon coast under different land uses: pristine mangroves, mangroves adjacent to shrimp farms, mangroves converted to shrimp farms and converted to pasture. Pristine mangroves are functioning by 67% of their full capacity into ecosystem boundaries, while pristine mangroves near shrimp farms are functioning by 64%, a sign of early degradation detection. Mangroves converted to shrimp farms are functioning by 52%, and, finally, those converted to pasture by 32%. A large soil dataset of eight indicators was required to detect an early stage of degradation in the mangroves adjacent to shrimp farms, while for the advanced degradation cases of shrimp farms and pasture only three indicators were able to detect the loss of soil multifunctionality. Converting mangroves to human-focused food production systems do not offer reasonable trade-offs to justify land exploration, since the converted sites reduced the delivery of ecosystem services to less than 30%. The index represents an effective alternative for surveying and monitoring degradation stages and ecosystem service losses in mangroves under land-use change.